Heatmap Visualisation troubleshooting

COVIRT19 microbial subgroup seqscreen analysis

Date : 23 DEC 2020

Maintained by :

Jochum, Michael D. 
Baylor College of Medicine 
michael.jochum@bcm.edu

Mike, thank you for walking me through this pheatmap stuff I actually found a couple bugs in the code that made it through.

compsitionally transform both datasets

prune out the masslin2 GO Terms and fix the names for the big dataset

order the count tables by the rowMeans

make an annotation dataset for the colum headers

make the annotation rows

make the associated color pallete for the column and row headers

heat map Ex 1:

They are similar, but arent exactly the same

heat map Ex 2:

zscore transformation make the differences look even more subtle, but there are still slight variances...

heat map Ex 3:

it looks the transforming the dataset before the subset yields nicer clustering based on case...

heat map Ex 4:

ok based on these results it looks like I want to use the dataset taht was compositionally transformed before subset, and I'm still on the fence about z-scoring.... \ Let me see if I can make a polished up version

heat map Ex 5:

Everything below her is Original STUFF

Ammendment that removes the publication coloumn

Chisq. test and factorial anova